getParams: Get pulseModel params

In pulseTD: Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data

Description

It is used to obtain the parameters of the pulse function J Comput Biol (2009 Feb) <doi:10.1089/cmb.2008.13TT>, including transcription parameters, degradation parameters and processing parameters. You can use these parameters to analyze transcriptional characteristics, including steady-state analysis. At the same time, you can use pulseModel to view the curve corresponding to the parameter.

Usage

getParams(object, stage, genename = NULL)

Arguments

object	a 'pulseTDmodel' that has been calculated with estimateParams
stage	A character is one of three stages of transcriptional dynamics, transcription, processing and degradation.
genename	a vector, default is NULL If it is NULL: Calculate the transcriptional dynamic rate of all genes If it is a gene vector: only calculate the transcriptional dynamic rate of a given gene vector If it is a numerical vector: only calculate the transcriptional dynamic rate of the gene corresponding to a given value.

Value

A matrix or vector containing six parameters: h0,h1,h2,t1 t2,beta

Examples

data('pulseRates', package='pulseTD')
TimeGrid <- c(0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180)
pulseRates_correct <- correctionParams(pulseRates)
transcription_params = getParams(pulseRates,'transcription')
degradation_params = getParams(pulseRates, 'degradation')
processing_params = getParams(pulseRates, 'processing')
head(transcription_params)
head(degradation_params)
head(processing_params)
transcription_params = getParams(pulseRates, 'transcription', genename=c(1,2,3))
head(transcription_params)
###
transcription_pulse = pulseModel(as.matrix(transcription_params[1,]), TimeGrid)
degradation_pulse = pulseModel(as.matrix(degradation_params[1,]), TimeGrid)
processing_pulse = pulseModel(as.matrix(processing_params[1,]), TimeGrid)

pulseTD documentation built on May 17, 2019, 5:03 p.m.